The Intercompany "Auto. Accept Transaction" function transfers documents, like Sales Invoices or Purchases Invoice, directly from the document in the sending company /IC partner into the document in the receiving IC partner, skipping the tasks in the IC Outbox on the sending end and also the tasks in the IC Inbox at receiving the IC partner.

But the feature does work the same way for IC Journal lines.
IC Journal lines will be transferred to the IC Inbox of the IC partner "only".
The reason is that there is no way to specify an "IC Auto. Accept Gen. Journal Template" and an " IC Auto. Accept Gen. Journal Batch" yet.